Applying feature coupling generalization for protein-protein interaction extraction

2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009

Volumn , Issue , 2009, Pages 396-400

  Li, Yanpeng ^a   Lin, Hongfei ^a   Yang, Zhihao ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Feature; Protein protein interaction extraction

Indexed keywords

BIOMEDICAL LITERATURE; CO-OCCURRENCE; COMBINED METHOD; FEATURE COUPLING; LABELED DATA; LEXICAL FEATURES; PROTEIN-PROTEIN INTERACTIONS; SEMI-SUPERVISED LEARNING; STATE-OF-THE-ART PERFORMANCE; SYNTACTIC INFORMATION; UNLABELED DATA;

BIOINFORMATICS; PROTEINS; SUPERVISED LEARNING;

FEATURE EXTRACTION;

EID: 74549142934     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2009.65     Document Type: Conference Paper

References (16)

1. A.M. Cohen and W.R. Hersh, "A Survey of Current Work in Biomedical Text Mining", Briefings in Bioinformatics, 2005, 6, pp. 57-71.
2. A. Airola, S. Pyysalo, J. Björne, T. Pahikkala, F. Ginter, and T. Salakoski, "All-paths Graph Kernel for Protein-protein Interaction Extraction with Evaluation of Cross-corpus Learning", BMC Bioinformatics, 2008, 9 (Suppl 11):S2.
3. Y. Miyao, R. Sætre, K. Sagae, T. Matsuzaki, and J. Tsujii, "Evaluating Contributions of Natural Language Parsers to Protein-Protein Interaction Extraction", Bioinformatics, 2009, 25(3), pp. 394-400.
4. M. Miwa, R. Sætre, Y. Miyao, T. Ohta, J. Tsujii, "Combining Multiple Layers of Syntactic Information for Protein-Protein Interaction Extraction", Proceedings of the Third International Symposium on Semantic Mining in Biomedicine, 2008, pp. 101-108.
5. M. Krallinger, F. Leitner, C. Rodriguez-Penagos, and A. Valencia, "Overview of the Protein-Protein Interaction Annotation Extraction Task of BioCreative II", Genome Biology, 2008, 9(Suppl 2):S4.
6. R.C. Bunescu and R. J. Mooney. "Collective Information Extraction with Relational Markov Networks", In ACL 2004, 2004, pp. 439-446.
7. T. Mitsumori, M. Murata, Y. Fukuda, K. Doi, and H. Doi. "Extracting Protein-Protein Interaction Information from Biomedical Text with SVM", IEICE - Transactions on Information and Systems, 2006, E89-D(8), pp. 2464-2466.
8. R. C. Bunescu and R. J. Mooney. "Subsequence Kernels for Relation Extraction", NIPS 2005, 2005.
9. R. Sætre, K. Sagae, and J. Tsujii. "Syntactic Features for Protein-Protein Interaction Extraction. In LBM 2007 short papers.
10. S.V. Landeghem, Y. Saeys, and Y.V. Peer. "Extracting Protein-Protein Interactions from Text using Rich Feature Vectors and Feature Selection", Proceedings of the Third International Symposium on Semantic Mining in Biomedicine, 2008, pp. 77-84.
11. R. C. Bunescu and R. J. Mooney, "A Shortest Path Dependency Kernel for Relation Extraction", In HLT/EMNLP, 2005, pp. 724-731.
12. Y. Li, H. Lin and Z. Yang. "Incorporating Rich Background Knowledge for Gene Named Entity Classification and Recognition", BMC Bioinformatics, 2009, 10:223.
13. S. Pyysalo, A. Airola, J. Heimonen, J. Björne, F. Ginter, and T. Salakoski, "Comparative Analysis of Five Protein-protein Interaction Corpora", BMC Bioinformatics, 2008, 9(Suppl 3):S6
14. T. Joachims, "Making large-Scale SVM Learning Practical", Advances in Kernel Methods - Support Vector Learning. B. Schölkopf and C. Burges and A. Smola (ed.), MIT-Press, 1999.
15. W. Hersh, A. Cohen, P. Roberts and H.K. Rekapalli: "TREC 2006 genomics track overview." Proceedings of 15th Text REtrieval Conference ((TREC), 2006.
16. J. Wilbur, L. Smith, and L. Tanabe, "BioCreative 2. gene mention task", Proceedings of the Second BioCreative Challenge Evaluation Workshop, 2007, pp. 7-16.